Question: Migrating 14.02 to 15.05 : KeyError: 'tool_test' after migrate_tools/0012_tools.sh
1
gravatar for jpvillemin
3.0 years ago by
jpvillemin10
France
jpvillemin10 wrote:

I'm trying to make an update ... I' have done the following commands.

hg pull
hg update -C latest_15.05
./run.sh
"Exception: Your database has version '118' but this code expects version '129'.  Please backup your database and then migrate the schema by running 'sh manage_db.sh -c ./universe_wsgi.ini upgrade'."
sh manage_db.sh -c ./universe_wsgi.ini upgrade

sh ./scripts/migrate_tools/0012_tools.sh -c universe_wsgi.ini install_dependencies

I have the following error and i don't know what it means :

No handlers could be found for logger "galaxy.tools.data"
Traceback (most recent call last):
  File "./scripts/migrate_tools/migrate_tools.py", line 21, in <module>
    app = MigrateToolsApplication( sys.argv[ 1 ] )
  File "/Users/galaxy_dev_user/galaxy-dist/lib/tool_shed/galaxy_install/migrate/common.py", line 41, in __init__
    self._configure_toolbox()
  File "/Users/galaxy_dev_user/galaxy-dist/lib/galaxy/config.py", line 748, in _configure_toolbox
    self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self )
  File "/Users/galaxy_dev_user/galaxy-dist/lib/galaxy/tools/__init__.py", line 106, in __init__
    app=app,
  File "/Users/galaxy_dev_user/galaxy-dist/lib/galaxy/tools/toolbox/base.py", line 78, in __init__
    self._load_tool_panel()
  File "/Users/galaxy_dev_user/galaxy-dist/lib/galaxy/tools/toolbox/base.py", line 312, in _load_tool_panel
    self.__add_tool_to_tool_panel( val, self._tool_panel, section=False )
  File "/Users/galaxy_dev_user/galaxy-dist/lib/galaxy/tools/toolbox/base.py", line 251, in __add_tool_to_tool_panel
    tool = self._tools_by_id[ tool_id ]
KeyError: 'tool_test'

Thanlks

error update install • 866 views
ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by jpvillemin10

No one has a little idea what's going on ? :-/

ADD REPLYlink written 3.0 years ago by jpvillemin10

Hold tight, we are working out who is the best person to help troubleshoot from our team. And the community may still jump in. It is now getting later on the East Coast, US, so a reply may come in the morning. Thanks for patience! Jen, Galaxy team

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Jennifer Hillman Jackson25k

Ohh ok sorry, thanks :)

If i comment this script section in tool_conf.xml, the command seems to work well :

sh ./scripts/migrate_tools/0012_tools.sh -c universe_wsgi.ini install_dependencies

 <!--
  <section id="tool_test" name="tool_test">
    <tool file="test/python_version.xml" />
  </section>-->

Then the run.sh method worked too...

Initialy, the run.sh was modified for use of an virtual env for python....

# added 2014/02/25  launches python virtualenv with python 2.6
. ~/galaxy_env/bin/activate

python --version

Now i'will try to modify the new run.sh for using the python env 2.6

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by jpvillemin10
1
gravatar for jpvillemin
3.0 years ago by
jpvillemin10
France
jpvillemin10 wrote:

 

sh ./scripts/migrate_tools/0012_tools.sh -c universe_wsgi.ini install_dependencies <!-- <section id="tool_test" name="tool_test"> <tool file="test/python_version.xml" /> </section>-->

ADD COMMENTlink written 3.0 years ago by jpvillemin10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 67 users visited in the last hour